The functionally conserved subcortical maternal complex (SCMC) is essential for early embryonic development in mammals. Reproductive disorders caused by pathogenic variants in NLRP5, TLE6 and OOEP, three core components of the SCMC, have attracted much attention over the past several years. Evaluating the pathogenicity of a missense variant in the SCMC is limited by the lack of information on its structure, although we recently solved the structure of the mouse SCMC and proposed that reproductive disorders caused by pathogenic variants are related to the destabilization of the SCMC core complex. Here we report the cryogenic electron microscopy structure of the human SCMC and uncover that the pyrin domain of NLRP5 is essential for the stability of SCMC. By combining prediction of SCMC stability and in vitro reconstitution, we provide a method for identifying deleterious variants, and we successfully identify a new pathogenic variant of TLE6 (p.A396T). Thus, on the basis of the structure of the human SCMC, we offer a strategy for the diagnosis of reproductive disorders and the discovery of new infertility-associated variants.

功能保守的皮层下母体复合体 （SCMC） 对于哺乳动物的早期胚胎发育至关重要。由 NLRP5、TLE6 和 OOEP 的致病性变异（SCMC 的三个核心组成部分）引起的生殖障碍在过去几年中引起了广泛关注。由于缺乏有关其结构的信息，评估 SCMC 中错义变异的致病性受到限制，尽管我们最近解决了小鼠 SCMC 的结构并提出由致病性变异引起的生殖障碍与 SCMC 核心复合物的不稳定有关。在这里，我们报道了人 SCMC 的低温电子显微镜结构，并发现 NLRP5 的 pyrin 结构域对 SCMC 的稳定性至关重要。通过结合 SCMC 稳定性的预测和体外重建，我们提供了一种识别有害变异的方法，并且我们成功鉴定了 TLE6 （p.A396T） 的新致病性变异。因此，基于人类 SCMC 的结构，我们提供了一种诊断生殖障碍和发现新的不孕症相关变异的策略。